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- PDB-8phd: Structure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP -

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Basic information

Entry
Database: PDB / ID: 8phd
TitleStructure of Human Cdc123 bound to domain 3 of eIF2 gamma and ATP
Components
  • Cell division cycle protein 123 homolog
  • Eukaryotic translation initiation factor 2 subunit 3
KeywordsTRANSLATION / eIF2 / translation initiation / chaperone / Cdc123 / ATP grasp
Function / homology
Function and homology information


eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / translation factor activity, RNA binding / protein-synthesizing GTPase ...eukaryotic translation initiation factor 2 complex assembly / Cellular response to mitochondrial stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / translation factor activity, RNA binding / protein-synthesizing GTPase / formation of translation preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / membrane scission GTPase motor activity / translation initiation factor activity / protein folding chaperone / translational initiation / PKR-mediated signaling / ABC-family proteins mediated transport / cadherin binding / GTPase activity / GTP binding / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 ...Cell division cycle protein 123 / D123 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Translation initiation factor eIF2 assembly protein / Eukaryotic translation initiation factor 2 subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSchmitt, E. / Mechulam, Y. / Cardenal Peralta, C. / Fagart, J. / Seufert, W.
Funding support France, Germany, 3items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)UMR7654 France
Ecole polytechniqueUMR7654 France
German Research Foundation (DFG) Germany
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Binding of human Cdc123 to eIF2 gamma.
Authors: Cardenal Peralta, C. / Vandroux, P. / Neumann-Arnold, L. / Panvert, M. / Fagart, J. / Seufert, W. / Mechulam, Y. / Schmitt, E.
History
DepositionJun 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle protein 123 homolog
B: Eukaryotic translation initiation factor 2 subunit 3
C: Cell division cycle protein 123 homolog
D: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4608
Polymers107,3974
Non-polymers1,0634
Water5,080282
1
A: Cell division cycle protein 123 homolog
B: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2304
Polymers53,6992
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-31 kcal/mol
Surface area20020 Å2
MethodPISA
2
C: Cell division cycle protein 123 homolog
D: Eukaryotic translation initiation factor 2 subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2304
Polymers53,6992
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-31 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.462, 126.020, 74.644
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cell division cycle protein 123 homolog / Protein D123 / HT-1080 / PZ32


Mass: 41349.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC123, C10orf7, D123 / Production host: Escherichia coli (E. coli) / References: UniProt: O75794
#2: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2-gamma X / eIF-2gX


Mass: 12349.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2S3, EIF2G / Production host: Escherichia coli (E. coli) / References: UniProt: P41091, protein-synthesizing GTPase
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 0.2 M lithium citrate 1 mM ATP 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→64.22 Å / Num. obs: 39743 / % possible obs: 93 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rrim(I) all: 0.151 / Net I/σ(I): 9.1
Reflection shellResolution: 2.08→2.37 Å / Num. unique obs: 1988 / CC1/2: 0.599

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→64.22 Å / Cross valid method: FREE R-VALUE / σ(F): 37.29 / Phase error: 25.8598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 2099 5.28 %
Rwork0.1764 37644 -
obs0.1788 39743 59.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.92 Å2
Refinement stepCycle: LAST / Resolution: 2.08→64.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6505 0 64 282 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166748
X-RAY DIFFRACTIONf_angle_d0.44139123
X-RAY DIFFRACTIONf_chiral_restr0.0396987
X-RAY DIFFRACTIONf_plane_restr0.00321146
X-RAY DIFFRACTIONf_dihedral_angle_d14.68672491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.143740.259497X-RAY DIFFRACTION2.06
2.14-2.190.2644230.3216249X-RAY DIFFRACTION5.29
2.19-2.260.3193170.2813429X-RAY DIFFRACTION8.97
2.26-2.330.2314310.2682710X-RAY DIFFRACTION14.82
2.33-2.410.267540.25461121X-RAY DIFFRACTION23.88
2.41-2.510.2492680.25261626X-RAY DIFFRACTION34.39
2.51-2.630.30251500.24162674X-RAY DIFFRACTION56.21
2.63-2.760.28291870.22123805X-RAY DIFFRACTION79.65
2.76-2.940.25342400.20224329X-RAY DIFFRACTION91.79
2.94-3.160.23662270.19734551X-RAY DIFFRACTION95.17
3.16-3.480.21872290.17994526X-RAY DIFFRACTION95.16
3.48-3.990.19972210.16434554X-RAY DIFFRACTION95.31
3.99-5.020.15882440.13654545X-RAY DIFFRACTION94.83
5.02-64.220.18512310.17454601X-RAY DIFFRACTION95.06
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.918196498670.4474325317710.04668465348351.98172136555-0.8077184782731.41702426706-0.014084967403-0.19139467838-0.1050311112220.1567996116370.0195081669186-0.006388381870230.132517286869-0.04111647472560.03486397124240.2379747904860.01470849715480.005961972931380.16995659320.05922053007520.17277676393612.36965951712.354945257446.8197214202
23.00300914750.617673267535-0.5116420325941.973496093-0.5406321494542.99587189535-0.2060906182370.513673931363-0.0232665213403-0.3592355202280.0747197234561-0.126258485010.1214093017830.006423447694560.1236469782350.26709613602-0.01222761733920.03432489363290.2916966617960.04670243691850.19750520598121.445662304417.367139192429.7127396609
33.991643647322.96809256527-2.524650743963.76498953086-0.0974421668593.7300792667-0.395416472439-0.5583918234430.0401015562173-1.46702121890.152837616708-0.2176915453141.99756361071-0.06853478940890.345732804630.6939019355940.0506730610628-0.09869976169720.485361115356-0.1197708712670.40568844425323.887661858115.367478428310.8444052833
47.295159553244.6715034445-6.295229326314.43427046617-3.210425573185.905189508680.07655751661290.03725295923320.1793135935380.144359254112-0.09859438363990.276078561635-0.0834005656981-0.2295800763290.05003395109920.670463711953-0.02580576610970.04806940616080.6393690683080.1049723051880.25318000035911.615029106219.022846275120.7180900215
57.54882276834-6.149231123163.961362591766.9585584779-2.199325772018.403050847750.8720003018620.620047879563-0.599428927881-1.14709298062-0.2613817685091.41222891410.415068312159-0.673581864576-0.4583219709590.4944163240280.167523645312-0.06255294871180.661491666032-0.002432962014420.518382725618-18.4544804280.59124855674831.8094157439
63.120448201311.935401627930.238780750079.421859290140.8520852163663.70709436624-0.109763276835-0.08811653413550.6289421283550.1723619826140.2332603429291.12814963489-0.233450559915-0.75534899358-0.1559418785320.2386334068740.08778770790640.0664444856740.4902997624080.1067336963450.426027519161-16.96245065215.9886128344.2192568178
75.043793444982.024115700370.9366435476743.964354722722.44458030082.700580500340.1940011021890.106888059826-1.226395962450.6697843755690.07600336341710.302961700331.1403867646-0.30446678827-0.1895199483290.439680919982-0.0616836396005-0.03802631673420.3088110378030.1858963531430.742714313719-10.7763405274-2.5730870054243.9150158454
86.801253478740.01721880802260.6798163165616.852213944211.308731521173.66425968834-0.2774104190590.3395671404120.449163359755-0.3674123365060.3551449465620.0959751204992-0.192652531658-0.814779965725-0.08203930360220.1555428387990.0291671924681-0.02160297443380.3315212413240.09016759297670.304431404797-9.1141381947112.777977716442.9857698898
97.68056594090.104405316972.024023647032.951750437071.770627091351.56209954695-0.00164574421463-0.07091795212640.660292002865-0.03777325511470.4003998874760.771404209331-0.11637566639-0.188418101123-0.1051654678480.2070765704110.0300126780611-0.05866489560050.5042586433350.1690746657940.498402753138-15.274751328916.247659160744.3211891782
106.96435473616-1.893344592850.41266749441.2007620962-0.4914859407464.057254113250.01131470353170.123805691880.124008914709-0.1049275852170.1933169903750.07932583314940.0815294609554-0.193413320533-0.207734510580.215071630157-0.03144887500160.002471555321890.2271874145850.07480929527790.38119286125-10.87666262578.9521467953641.2624661011
113.69615888659-0.6110535072620.8851647995072.07326589459-1.024030084941.62248805465-0.005943328543420.2270881185030.277194383158-0.1301166347130.0576984288310.0107558781043-0.1230732841460.06348777506310.02600740188330.2418431840040.01671236386620.05277852186080.228441276670.0849374056450.18592225060327.1181298544-12.3311609887-8.93703331153
123.27244690975-0.6889959372890.03855039486553.98279611862-0.1911989756133.64881355054-0.00787718401579-0.2073719933090.5110713518780.147478932743-0.167885605934-0.334712007607-0.6721410106830.2363766154440.1608367860060.26745331767-0.00456671630396-0.02361925170380.2868662571450.06059164929430.25666052294532.3856905733-9.02705596394-0.870519121579
134.04396433346-0.02169665879360.3972683131973.77797654160.001737840112253.94360059332-0.0645188379021-0.278298954129-0.05480362302040.429328835097-0.0340677493106-0.11632959839-0.03621546164670.1460184224070.09893945429670.2698931572520.03312742810670.01611432994280.2543699570980.1057670534840.18947159326138.7366521441-22.27372614611.4573756357
141.777945407531.10899686845-2.305562284818.76479801021-3.924781789674.40255409642-0.154782905331-1.1686042354-0.3583947308030.871331102309-0.280991156801-0.891827265507-0.6079112928270.2330726499640.5086829162280.6571000485130.00256034302179-0.07872749764460.6725716513690.07693979380910.30912674423236.9199702504-20.849993250524.5393901491
153.30475436998-4.15459173625-0.5528412186915.244833323060.4432140201463.131823615110.164036055221-1.423276380920.2931214041350.155867638770.1479362688440.328019157193-0.3525030141880.176557860242-0.2281809661920.580029552325-0.1310348779520.2047873556430.865424232931-0.05641620909120.7079374914752.97465506821-5.226337952946.078831538
163.085591604911.184128673780.4936787146477.04484864770.3728385696782.11643407003-0.106157528044-0.168342938304-0.3852933903370.352412136110.3550997175491.229066745760.0605136507299-0.450473143933-0.2200218885750.278018503517-0.04611573665980.1178026195460.4532670127840.170261753030.46770383834-1.51638294423-14.0247062081-6.4248957431
174.08727636529-2.222733324271.279802211115.199561815010.218775131545.67744522991-0.0068732463783-0.1659057183551.196628540480.281061200690.5989387750490.465845903691-1.39851308382-0.176499786015-0.2605253297920.5870705652660.05707370327250.2305021546390.2877498047570.1155956640260.7889361330744.921770422276.149487583-2.64463425234
183.75151439102-0.659924692791-0.02325820721452.509115675432.303072883153.195143570980.0339914564654-0.1159662182180.4627529367920.1101018197460.4282247144980.8094118974950.0594553487316-0.317148634903-0.4380922605670.20359706542-0.02759152693840.09250960881690.2753653286010.1114253759420.5044360235735.91685726411-9.70496584406-7.35923496032
194.538604478910.532033237730.7154893273514.97881114285-2.262344683968.55437206829-0.2131645514450.0287988923345-0.23481843438-0.0578373051370.188646090302-0.2461563880170.192990015211-0.1395268204140.1072485183810.229784839556-0.03918840280490.1164461633920.3745829180510.1851264556210.334449369315.59428367393-13.794088557-9.31454182194
204.586780761330.686040229081-1.167660024213.075642173232.223514626482.26024596938-0.229052439706-0.736372586971-0.184011709826-0.08311049145460.3379685916020.6551583076310.23453569529-0.749356940118-0.1160520024290.2491482098310.004318613024560.02991571835460.391487100640.2181101174470.5511483008670.125312001538-17.1670918806-7.03496577742
212.749011286273.94560735687-0.1946136605315.95349366331-0.4003301007952.990714013270.380239151173-0.6507306746380.2403853246870.287535615518-0.1789699816020.387227471573-0.536007849418-0.355032216681-0.1162724876670.2756963180920.0773766409150.08238819696310.3379798437460.09709277098380.3773601832386.9626277279-5.49326395914-1.9672915795
225.48043670553-3.46458004695-0.4964151367989.736035420572.213477114285.192678883370.259074419539-0.254933363701-1.65507729099-0.2204309690370.3475480466670.6476757920850.803436729436-0.519566104661-0.4558140228960.400599187936-0.0630825390386-0.01879374982710.4011065634680.1498488520530.683512610898-3.47249701876-22.0015992132-9.21587396749
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 136 )AA0 - 1361 - 115
22chain 'A' and (resid 137 through 260 )AA137 - 260116 - 239
33chain 'A' and (resid 261 through 276 )AA261 - 276240 - 255
44chain 'A' and (resid 277 through 318 )AA277 - 318256 - 283
55chain 'A' and (resid 319 through 336 )AA319 - 336284 - 301
66chain 'B' and (resid 365 through 377 )BD365 - 3771 - 13
77chain 'B' and (resid 378 through 402 )BD378 - 40214 - 31
88chain 'B' and (resid 403 through 420 )BD403 - 42032 - 49
99chain 'B' and (resid 421 through 439 )BD421 - 43950 - 68
1010chain 'B' and (resid 440 through 465 )BD440 - 46569 - 94
1111chain 'C' and (resid -4 through 136 )CE-4 - 1361 - 122
1212chain 'C' and (resid 137 through 176 )CE137 - 176123 - 162
1313chain 'C' and (resid 177 through 260 )CE177 - 260163 - 246
1414chain 'C' and (resid 261 through 301 )CE261 - 301247 - 281
1515chain 'C' and (resid 302 through 334 )CE302 - 334282 - 306
1616chain 'D' and (resid 365 through 379 )DH365 - 3791 - 15
1717chain 'D' and (resid 380 through 396 )DH380 - 39616 - 25
1818chain 'D' and (resid 397 through 410 )DH397 - 41026 - 39
1919chain 'D' and (resid 411 through 420 )DH411 - 42040 - 49
2020chain 'D' and (resid 421 through 439 )DH421 - 43950 - 68
2121chain 'D' and (resid 440 through 458 )DH440 - 45869 - 87
2222chain 'D' and (resid 459 through 465 )DH459 - 46588 - 94

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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